Complete mitochondrial genome sequences of  threeNakaseomycesspecies reveal invasion by palindromic GC clusters and considerable size expansion

Abstract

Here we report the sequence of three mitochondrial genomes from yeasts of the Nakaseomyces clade that includes the pathogenic yeast Candida glabrata, namely, that of Kluyveromyces delphensis, Candida castellii and Kluyveromyces bacillisporus. The gene content is equivalent to that of C. glabrata, but reveals the existence of new group I introns in COX1 and CYTB and new potential intronic endonucleases. Gene order is highly rearranged in these genomes, which contain numerous palindromic GC clusters. The more GC nucleotides these elements contain, the longer and more AT-rich are the intergenes containing them, leading to a direct relationship between the number of Gs and Cs within the elements and the size of the genomes. Thus, there is a fivefold difference in size between the smallest and the largest mitochondrial genome, with the largest being the most AT-rich overall. Sequences are available under EMBL accession numbers FM995164, FM995165, and FM995166.

Population Genomic Analysis Reveals Highly Conserved Mitochondrial Genomes in the Yeast Species Lachancea thermotolerans

“…Comparative analysis across seven Lachancea species, concluded that ultimately, mt genome evolution is mostly related to intron motility and intergenic region variation. This finding was reported in other instances as well, both between closely and distantly related species (Bouchier et al 2009; Gaillardin et al 2012). …”

Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

“…This size variation is correlated with either the relative size of intergenic sequences or the intron content (Table 1). By contrast to the genomes of the Nakaseomyces clade, we did not observe a relation between the number of GC clusters and the size of these genomes (data not shown) [23]. Intergenic regions range from 23.1% in L. mirantina to 58% in L. kluyveri .…”

“…The synteny varies considerably within Hemiascomycetes, which reflects small rearrangements occurring in the history of hemiascomycete fungi. As an example, gene order is highly rearranged in the mt genomes of yeasts of the Nakaseomyces clade [23]. Inversion as well as movement of short intergenic repeat and mobile introns seems to be at the origin of this variability [24].…”

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

“…In C. glabrata , the CGN-codon family has been entirely eliminated due to the loss of the cognate tRNA molecule (Koszul et al 2003). Considerable size variation of mtDNA molecules is also observed between related species, ranging from ∼20 kb in C. glabrata to almost 110 kb in Nakaseomyces bacillisporus (Bouchier et al 2009). Size variation is due in part to the presence/absence of group-I and group-II introns.…”

“…Size variation is due in part to the presence/absence of group-I and group-II introns. But it also results from the invasion of short GC-rich palindromic clusters of unclear origin associated with the expansion of large AT-rich intergenic regions (Bouchier et al 2009). These elements were discovered long ago in S. cerevisiae (Dujon 1981), but their patchy distribution across the entire phylogeny of Saccharomycotina species (Freel et al 2015) raises an interesting problem to examine.…”